Per chromosome imputation report for cohort WTCCC_cohort.
Chromosome index, 23 in total. Skip to the section for a particular chromosome using the buttons below.
Information captured during the processing of this cohort.
| Property | Value |
|---|---|
| FORMAT | MINIMAC2 |
| UPLOADED | 12.4.2021 |
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 17883586 | 79.546 |
| 0.1 | 1221147 | 5.432 |
| 0.2 | 810985 | 3.607 |
| 0.3 | 617510 | 2.747 |
| 0.4 | 495321 | 2.203 |
| 0.5 | 405361 | 1.803 |
| 0.6 | 348819 | 1.552 |
| 0.7 | 290679 | 1.293 |
| 0.8 | 241173 | 1.073 |
| 0.9 | 167605 | 0.746 |
| Total | 22482186 | 100.000 |
Variants binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 1367935 | 6.085 |
| 0.4 | 1630497 | 7.252 |
| 0.5 | 2131252 | 9.480 |
| 0.6 | 2760289 | 12.278 |
| 0.7 | 3277116 | 14.577 |
| 0.8 | 3534860 | 15.723 |
| 0.9 | 7750740 | 34.475 |
| 1.0 | 29497 | 0.131 |
| Total | 22482186 | 100.000 |
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 1363728 | 79.9709 |
| 0.1 | 89352 | 5.2397 |
| 0.2 | 57866 | 3.3933 |
| 0.3 | 45395 | 2.6620 |
| 0.4 | 37499 | 2.1990 |
| 0.5 | 30402 | 1.7828 |
| 0.6 | 27078 | 1.5879 |
| 0.7 | 21694 | 1.2722 |
| 0.8 | 18605 | 1.0910 |
| 0.9 | 13661 | 0.8011 |
| Total | 1705280 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 104530 | 6.1298 |
| 0.4 | 126335 | 7.4085 |
| 0.5 | 163078 | 9.5631 |
| 0.6 | 212129 | 12.4395 |
| 0.7 | 252549 | 14.8098 |
| 0.8 | 269738 | 15.8178 |
| 0.9 | 574761 | 33.7048 |
| 1.0 | 2160 | 0.1267 |
| Total | 1705280 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 1521939 | 80.2644 |
| 0.1 | 100514 | 5.3009 |
| 0.2 | 66172 | 3.4898 |
| 0.3 | 49378 | 2.6041 |
| 0.4 | 38639 | 2.0378 |
| 0.5 | 32735 | 1.7264 |
| 0.6 | 28710 | 1.5141 |
| 0.7 | 23365 | 1.2322 |
| 0.8 | 20136 | 1.0619 |
| 0.9 | 14570 | 0.7684 |
| Total | 1896158 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 107228 | 5.6550 |
| 0.4 | 129251 | 6.8165 |
| 0.5 | 171099 | 9.0235 |
| 0.6 | 229462 | 12.1014 |
| 0.7 | 281585 | 14.8503 |
| 0.8 | 302173 | 15.9361 |
| 0.9 | 672952 | 35.4903 |
| 1.0 | 2408 | 0.1270 |
| Total | 1896158 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 1283134 | 79.8705 |
| 0.1 | 87675 | 5.4575 |
| 0.2 | 55282 | 3.4411 |
| 0.3 | 43175 | 2.6875 |
| 0.4 | 34872 | 2.1707 |
| 0.5 | 29254 | 1.8210 |
| 0.6 | 24710 | 1.5381 |
| 0.7 | 20480 | 1.2748 |
| 0.8 | 16581 | 1.0321 |
| 0.9 | 11355 | 0.7068 |
| Total | 1606518 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 89473 | 5.5694 |
| 0.4 | 106131 | 6.6063 |
| 0.5 | 143733 | 8.9469 |
| 0.6 | 193368 | 12.0365 |
| 0.7 | 237125 | 14.7602 |
| 0.8 | 257980 | 16.0583 |
| 0.9 | 576551 | 35.8882 |
| 1.0 | 2157 | 0.1343 |
| Total | 1606518 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 1240741 | 79.0174 |
| 0.1 | 82050 | 5.2254 |
| 0.2 | 60614 | 3.8602 |
| 0.3 | 44901 | 2.8595 |
| 0.4 | 34088 | 2.1709 |
| 0.5 | 27850 | 1.7736 |
| 0.6 | 24426 | 1.5556 |
| 0.7 | 21621 | 1.3769 |
| 0.8 | 19860 | 1.2648 |
| 0.9 | 14062 | 0.8955 |
| Total | 1570213 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 89060 | 5.6718 |
| 0.4 | 105898 | 6.7442 |
| 0.5 | 141483 | 9.0104 |
| 0.6 | 186958 | 11.9065 |
| 0.7 | 227001 | 14.4567 |
| 0.8 | 249942 | 15.9177 |
| 0.9 | 568203 | 36.1864 |
| 1.0 | 1668 | 0.1062 |
| Total | 1570213 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 1162069 | 79.8972 |
| 0.1 | 76955 | 5.2910 |
| 0.2 | 53080 | 3.6495 |
| 0.3 | 40328 | 2.7727 |
| 0.4 | 31697 | 2.1793 |
| 0.5 | 24614 | 1.6923 |
| 0.6 | 22361 | 1.5374 |
| 0.7 | 18267 | 1.2559 |
| 0.8 | 14955 | 1.0282 |
| 0.9 | 10129 | 0.6964 |
| Total | 1454455 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 81267 | 5.5875 |
| 0.4 | 95870 | 6.5915 |
| 0.5 | 127869 | 8.7915 |
| 0.6 | 171271 | 11.7756 |
| 0.7 | 211765 | 14.5597 |
| 0.8 | 233386 | 16.0463 |
| 0.9 | 530779 | 36.4933 |
| 1.0 | 2248 | 0.1546 |
| Total | 1454455 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 1115699 | 78.9240 |
| 0.1 | 81743 | 5.7825 |
| 0.2 | 52786 | 3.7341 |
| 0.3 | 40174 | 2.8419 |
| 0.4 | 32778 | 2.3187 |
| 0.5 | 25751 | 1.8216 |
| 0.6 | 22684 | 1.6047 |
| 0.7 | 17077 | 1.2080 |
| 0.8 | 15205 | 1.0756 |
| 0.9 | 9741 | 0.6891 |
| Total | 1413638 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 72812 | 5.1507 |
| 0.4 | 85374 | 6.0393 |
| 0.5 | 116125 | 8.2146 |
| 0.6 | 158164 | 11.1884 |
| 0.7 | 199091 | 14.0836 |
| 0.8 | 224170 | 15.8577 |
| 0.9 | 555698 | 39.3098 |
| 1.0 | 2204 | 0.1559 |
| Total | 1413638 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 1005463 | 79.3690 |
| 0.1 | 69640 | 5.4972 |
| 0.2 | 47563 | 3.7545 |
| 0.3 | 35564 | 2.8073 |
| 0.4 | 28532 | 2.2523 |
| 0.5 | 23597 | 1.8627 |
| 0.6 | 18910 | 1.4927 |
| 0.7 | 16320 | 1.2883 |
| 0.8 | 12183 | 0.9617 |
| 0.9 | 9049 | 0.7143 |
| Total | 1266821 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 77010 | 6.0790 |
| 0.4 | 90495 | 7.1435 |
| 0.5 | 119327 | 9.4194 |
| 0.6 | 154921 | 12.2291 |
| 0.7 | 184826 | 14.5897 |
| 0.8 | 200664 | 15.8400 |
| 0.9 | 438268 | 34.5959 |
| 1.0 | 1310 | 0.1034 |
| Total | 1266821 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 992708 | 80.0723 |
| 0.1 | 64037 | 5.1653 |
| 0.2 | 44350 | 3.5773 |
| 0.3 | 32645 | 2.6332 |
| 0.4 | 27620 | 2.2278 |
| 0.5 | 21361 | 1.7230 |
| 0.6 | 19367 | 1.5622 |
| 0.7 | 15544 | 1.2538 |
| 0.8 | 13131 | 1.0592 |
| 0.9 | 9002 | 0.7261 |
| Total | 1239765 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 71751 | 5.7875 |
| 0.4 | 84039 | 6.7786 |
| 0.5 | 108521 | 8.7534 |
| 0.6 | 145481 | 11.7346 |
| 0.7 | 181951 | 14.6762 |
| 0.8 | 196112 | 15.8185 |
| 0.9 | 450260 | 36.3182 |
| 1.0 | 1650 | 0.1331 |
| Total | 1239765 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 753977 | 79.6899 |
| 0.1 | 53745 | 5.6805 |
| 0.2 | 34056 | 3.5995 |
| 0.3 | 24789 | 2.6200 |
| 0.4 | 20374 | 2.1534 |
| 0.5 | 15717 | 1.6612 |
| 0.6 | 14756 | 1.5596 |
| 0.7 | 11663 | 1.2327 |
| 0.8 | 9683 | 1.0234 |
| 0.9 | 7379 | 0.7799 |
| Total | 946139 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 52467 | 5.5454 |
| 0.4 | 62368 | 6.5918 |
| 0.5 | 84587 | 8.9402 |
| 0.6 | 114539 | 12.1059 |
| 0.7 | 140305 | 14.8292 |
| 0.8 | 154762 | 16.3572 |
| 0.9 | 335904 | 35.5026 |
| 1.0 | 1207 | 0.1276 |
| Total | 946139 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 881072 | 79.4987 |
| 0.1 | 61009 | 5.5048 |
| 0.2 | 39577 | 3.5710 |
| 0.3 | 28729 | 2.5922 |
| 0.4 | 24734 | 2.2317 |
| 0.5 | 20875 | 1.8835 |
| 0.6 | 16857 | 1.5210 |
| 0.7 | 14276 | 1.2881 |
| 0.8 | 12571 | 1.1343 |
| 0.9 | 8585 | 0.7746 |
| Total | 1108285 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 59700 | 5.3867 |
| 0.4 | 70566 | 6.3671 |
| 0.5 | 94129 | 8.4932 |
| 0.6 | 127331 | 11.4890 |
| 0.7 | 159015 | 14.3478 |
| 0.8 | 176982 | 15.9690 |
| 0.9 | 418531 | 37.7638 |
| 1.0 | 2031 | 0.1833 |
| Total | 1108285 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 868549 | 79.4186 |
| 0.1 | 59196 | 5.4128 |
| 0.2 | 36204 | 3.3104 |
| 0.3 | 30720 | 2.8090 |
| 0.4 | 24374 | 2.2287 |
| 0.5 | 20709 | 1.8936 |
| 0.6 | 17952 | 1.6415 |
| 0.7 | 14417 | 1.3183 |
| 0.8 | 12151 | 1.1111 |
| 0.9 | 9362 | 0.8560 |
| Total | 1093634 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 61522 | 5.6255 |
| 0.4 | 73032 | 6.6779 |
| 0.5 | 98616 | 9.0173 |
| 0.6 | 130943 | 11.9732 |
| 0.7 | 159241 | 14.5607 |
| 0.8 | 171313 | 15.6646 |
| 0.9 | 396572 | 36.2619 |
| 1.0 | 2395 | 0.2190 |
| Total | 1093634 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 838212 | 79.6281 |
| 0.1 | 57055 | 5.4201 |
| 0.2 | 35524 | 3.3747 |
| 0.3 | 30740 | 2.9202 |
| 0.4 | 22760 | 2.1621 |
| 0.5 | 18841 | 1.7898 |
| 0.6 | 16360 | 1.5542 |
| 0.7 | 12460 | 1.1837 |
| 0.8 | 12468 | 1.1844 |
| 0.9 | 8239 | 0.7827 |
| Total | 1052659 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 60443 | 5.7419 |
| 0.4 | 71868 | 6.8273 |
| 0.5 | 93218 | 8.8555 |
| 0.6 | 125299 | 11.9031 |
| 0.7 | 151097 | 14.3538 |
| 0.8 | 167225 | 15.8860 |
| 0.9 | 381869 | 36.2766 |
| 1.0 | 1640 | 0.1558 |
| Total | 1052659 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 624079 | 78.7205 |
| 0.1 | 42931 | 5.4153 |
| 0.2 | 28051 | 3.5383 |
| 0.3 | 22752 | 2.8699 |
| 0.4 | 17566 | 2.2158 |
| 0.5 | 15501 | 1.9553 |
| 0.6 | 12609 | 1.5905 |
| 0.7 | 11381 | 1.4356 |
| 0.8 | 9689 | 1.2222 |
| 0.9 | 8219 | 1.0367 |
| Total | 792778 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 41607 | 5.2483 |
| 0.4 | 49887 | 6.2927 |
| 0.5 | 68720 | 8.6683 |
| 0.6 | 93770 | 11.8280 |
| 0.7 | 117540 | 14.8263 |
| 0.8 | 129254 | 16.3039 |
| 0.9 | 290558 | 36.6506 |
| 1.0 | 1442 | 0.1819 |
| Total | 792778 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 555507 | 79.4550 |
| 0.1 | 38951 | 5.5712 |
| 0.2 | 26286 | 3.7597 |
| 0.3 | 18063 | 2.5836 |
| 0.4 | 15499 | 2.2168 |
| 0.5 | 11876 | 1.6986 |
| 0.6 | 10145 | 1.4511 |
| 0.7 | 9045 | 1.2937 |
| 0.8 | 7779 | 1.1126 |
| 0.9 | 5996 | 0.8576 |
| Total | 699147 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 41527 | 5.9397 |
| 0.4 | 50327 | 7.1983 |
| 0.5 | 65680 | 9.3943 |
| 0.6 | 86439 | 12.3635 |
| 0.7 | 101437 | 14.5087 |
| 0.8 | 108864 | 15.5710 |
| 0.9 | 244071 | 34.9098 |
| 1.0 | 802 | 0.1147 |
| Total | 699147 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 497379 | 79.6223 |
| 0.1 | 33362 | 5.3407 |
| 0.2 | 22368 | 3.5808 |
| 0.3 | 16706 | 2.6744 |
| 0.4 | 14279 | 2.2858 |
| 0.5 | 11781 | 1.8859 |
| 0.6 | 8956 | 1.4337 |
| 0.7 | 7909 | 1.2661 |
| 0.8 | 6557 | 1.0497 |
| 0.9 | 5376 | 0.8606 |
| Total | 624673 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 39694 | 6.3544 |
| 0.4 | 48588 | 7.7781 |
| 0.5 | 63162 | 10.1112 |
| 0.6 | 79441 | 12.7172 |
| 0.7 | 92256 | 14.7687 |
| 0.8 | 97455 | 15.6010 |
| 0.9 | 203165 | 32.5234 |
| 1.0 | 912 | 0.1460 |
| Total | 624673 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 531407 | 79.5658 |
| 0.1 | 37800 | 5.6597 |
| 0.2 | 22841 | 3.4199 |
| 0.3 | 19144 | 2.8664 |
| 0.4 | 13968 | 2.0914 |
| 0.5 | 12145 | 1.8184 |
| 0.6 | 10688 | 1.6003 |
| 0.7 | 9490 | 1.4209 |
| 0.8 | 6365 | 0.9530 |
| 0.9 | 4036 | 0.6043 |
| Total | 667884 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 46776 | 7.0036 |
| 0.4 | 55760 | 8.3488 |
| 0.5 | 71138 | 10.6513 |
| 0.6 | 87937 | 13.1665 |
| 0.7 | 99471 | 14.8935 |
| 0.8 | 106750 | 15.9833 |
| 0.9 | 199621 | 29.8886 |
| 1.0 | 431 | 0.0645 |
| Total | 667884 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 450966 | 79.2172 |
| 0.1 | 30181 | 5.3016 |
| 0.2 | 23026 | 4.0448 |
| 0.3 | 15475 | 2.7184 |
| 0.4 | 13550 | 2.3802 |
| 0.5 | 11131 | 1.9553 |
| 0.6 | 8798 | 1.5455 |
| 0.7 | 7907 | 1.3890 |
| 0.8 | 5654 | 0.9932 |
| 0.9 | 2590 | 0.4550 |
| Total | 569278 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 50109 | 8.8022 |
| 0.4 | 59949 | 10.5307 |
| 0.5 | 73375 | 12.8891 |
| 0.6 | 81629 | 14.3390 |
| 0.7 | 83371 | 14.6450 |
| 0.8 | 83580 | 14.6818 |
| 0.9 | 136987 | 24.0633 |
| 1.0 | 278 | 0.0488 |
| Total | 569278 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 488739 | 79.0812 |
| 0.1 | 33938 | 5.4914 |
| 0.2 | 23458 | 3.7957 |
| 0.3 | 17664 | 2.8582 |
| 0.4 | 13891 | 2.2477 |
| 0.5 | 11068 | 1.7909 |
| 0.6 | 9492 | 1.5359 |
| 0.7 | 8001 | 1.2946 |
| 0.8 | 6588 | 1.0660 |
| 0.9 | 5183 | 0.8386 |
| Total | 618022 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 36980 | 5.9836 |
| 0.4 | 45052 | 7.2897 |
| 0.5 | 61223 | 9.9063 |
| 0.6 | 79381 | 12.8444 |
| 0.7 | 91885 | 14.8676 |
| 0.8 | 97383 | 15.7572 |
| 0.9 | 205454 | 33.2438 |
| 1.0 | 664 | 0.1074 |
| Total | 618022 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 330738 | 77.5563 |
| 0.1 | 28370 | 6.6526 |
| 0.2 | 18677 | 4.3797 |
| 0.3 | 12922 | 3.0301 |
| 0.4 | 9596 | 2.2502 |
| 0.5 | 8211 | 1.9254 |
| 0.6 | 6667 | 1.5634 |
| 0.7 | 5766 | 1.3521 |
| 0.8 | 3920 | 0.9192 |
| 0.9 | 1582 | 0.3710 |
| Total | 426449 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 48173 | 11.2963 |
| 0.4 | 55115 | 12.9242 |
| 0.5 | 60871 | 14.2739 |
| 0.6 | 61150 | 14.3393 |
| 0.7 | 57222 | 13.4183 |
| 0.8 | 57067 | 13.3819 |
| 0.9 | 86635 | 20.3154 |
| 1.0 | 216 | 0.0507 |
| Total | 426449 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 390563 | 79.5883 |
| 0.1 | 27273 | 5.5576 |
| 0.2 | 18086 | 3.6855 |
| 0.3 | 13442 | 2.7392 |
| 0.4 | 11179 | 2.2780 |
| 0.5 | 8901 | 1.8138 |
| 0.6 | 7648 | 1.5585 |
| 0.7 | 5973 | 1.2172 |
| 0.8 | 4655 | 0.9486 |
| 0.9 | 3009 | 0.6132 |
| Total | 490729 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 31992 | 6.5193 |
| 0.4 | 39651 | 8.0800 |
| 0.5 | 52008 | 10.5981 |
| 0.6 | 65353 | 13.3175 |
| 0.7 | 71748 | 14.6207 |
| 0.8 | 74778 | 15.2381 |
| 0.9 | 154727 | 31.5300 |
| 1.0 | 472 | 0.0962 |
| Total | 490729 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 225870 | 78.1430 |
| 0.1 | 15736 | 5.4441 |
| 0.2 | 10151 | 3.5119 |
| 0.3 | 9027 | 3.1230 |
| 0.4 | 7217 | 2.4968 |
| 0.5 | 5965 | 2.0637 |
| 0.6 | 4875 | 1.6866 |
| 0.7 | 4482 | 1.5506 |
| 0.8 | 4000 | 1.3839 |
| 0.9 | 1724 | 0.5964 |
| Total | 289047 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 19731 | 6.8262 |
| 0.4 | 23407 | 8.0980 |
| 0.5 | 31530 | 10.9083 |
| 0.6 | 39021 | 13.4999 |
| 0.7 | 42242 | 14.6142 |
| 0.8 | 42875 | 14.8332 |
| 0.9 | 89821 | 31.0749 |
| 1.0 | 420 | 0.1453 |
| Total | 289047 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 219380 | 78.6055 |
| 0.1 | 15903 | 5.6982 |
| 0.2 | 11130 | 3.9880 |
| 0.3 | 7945 | 2.8468 |
| 0.4 | 6913 | 2.4770 |
| 0.5 | 5239 | 1.8772 |
| 0.6 | 4687 | 1.6794 |
| 0.7 | 3909 | 1.4006 |
| 0.8 | 2593 | 0.9291 |
| 0.9 | 1391 | 0.4984 |
| Total | 279090 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 23538 | 8.4338 |
| 0.4 | 27546 | 9.8699 |
| 0.5 | 33626 | 12.0484 |
| 0.6 | 39683 | 14.2187 |
| 0.7 | 40110 | 14.3717 |
| 0.8 | 40153 | 14.3871 |
| 0.9 | 74253 | 26.6054 |
| 1.0 | 181 | 0.0649 |
| Total | 279090 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 541667 | 80.6623 |
| 0.1 | 33731 | 5.0231 |
| 0.2 | 23837 | 3.5497 |
| 0.3 | 17832 | 2.6555 |
| 0.4 | 13696 | 2.0395 |
| 0.5 | 11837 | 1.7627 |
| 0.6 | 10083 | 1.5015 |
| 0.7 | 9632 | 1.4343 |
| 0.8 | 5844 | 0.8703 |
| 0.9 | 3365 | 0.5011 |
| Total | 671524 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 60545 | 9.0161 |
| 0.4 | 73988 | 11.0179 |
| 0.5 | 88134 | 13.1245 |
| 0.6 | 96619 | 14.3880 |
| 0.7 | 94283 | 14.0402 |
| 0.8 | 92254 | 13.7380 |
| 0.9 | 165100 | 24.5859 |
| 1.0 | 601 | 0.0895 |
| Total | 671524 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering